Datasets

The scripts are now supporting multiple angles, multiple channels and multiple illumination direction without adjusting the Snakefile or .bsh scripts.

Based on SPIM registration version 3.3.9

Supported datasets are in the following format:

ImageJ Opener (resave to .tif):

Multiple timepoints: YES (one file per timepoint)
Multiple channels: YES (one file per channel)
Multiple illumination directions: YES (one file per illumination direction) => not tested yet
Multiple angles: YES one file per angle

Zeiss Lightsheet Z.1 Dataset (LOCI)

Multiple timepoints: Supports multiple time points per file
Multiple channels: Supports multiple channels per file
Multiple illumination directions: YES (one file per illumination direction)
Multiple angles: YES (one file per angle)

Timelapse based workflow

Expected setup

Clone the repository:

The repository contains the example configuration scripts for single and dual channel datasets, the Snakefile which defines the workflow, the beanshell scripts which drive the processing via Fiji and a cluster.json file which contains information for the cluster queuing system.

/path/to/repo/timelapse
├── single_test.yaml
├── dual_OneChannel.yaml
├── Snakefile
├── cluster.json
├── define_tif_zip.bsh
├── define_czi.bsh
├── registration.bsh
├── deconvolution.bsh
├── transform.bsh	 		
├── registration.bsh 		
└── xml_merge.bsh	 		

A data directory e.g. looks like this:

It contains the .yaml file for the specific dataset. You can either copy it if you want to keep it together with the dataset or make a symlink from the processing repository.

/path/to/data
├── dataset.czi
├── dataset(1).czi
├── dataset(2).czi
├── dataset(3).czi
├── dataset(4).czi
└── dataset.yaml	 		# copied/symlinked from this repo

• tomancak.yaml contains the parameters that configure the beanshell scripts found in the data directory
• Snakefile from this directory
• cluster.json that resides in the same directory as the Snakefile
• cluster runs LSF

Tools:

The tool directory contains scripts for common file format pre-processing. Some datasets are currently only usable when resaving them into .tif:

• discontinous .czi datasets
• .czi dataset with multiple groups

The master_preprocesing.sh file is the configuration script that contains the information about the dataset that needs to be resaved or split. rename-zeiss-file.sh is renaming the .czi files into the .tif naming convention for SPIM processing: SPIM_TL{t}_Angle{a}.tif. The different resaving steps are then carried out by creating the jobs and submitting them to the cluster.

/path/to/repo/tools
├── master_preprocessing.sh
├── rename-zeiss-file.sh
├── compress
    ├── create-compress-jobs.sh
    ├── for_czi.bsh
    └── submit-jobs
├── czi_resave
    ├── create-resaving-jobs.sh
    ├── resaving.bsh
    └── submit-jobs
└──  split_channels
    ├── create-split-jobs.sh
    ├── split.bsh
    └── submit.jobs

Submitting Jobs

If DRMAA is supported on your cluster:

snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra}"

If not:

snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra}"